On Fri, Sep 25, 2015 at 11:08 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Hello Jason,
>
> Thank you a lot for the answer, I’ll check it carefully.
>
> If I understand well then, with the input file I’m using, the three water
> molecules in the QM region aren’t constrained: nor by shake (because of the
> noshakemask) neither by settle (because of jfastw=4) and the rest of the
> water molecules are constrained using shake, is that right?
>
> If so, is there any way to remove the constrains using settle from the
> three water molecules in the QM region only? Because when I run the same
> molecular dynamics simulation without jfastw=4 I don’t have this problem
> (even though the run is not over yet..).
>
It's a little complicated, but it can be done. sander identifies water
molecules that need to be dispatched to SETTLE by atom and residue name.
So if you change the residue names of the three waters you don't want to
SETTLE to something different (maybe QMW for QM water), that should do it.
You can either do this by hand in the prmtop file (look for the
RESIDUE_LABEL section), or using ParmEd in a Python program.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 25 2015 - 08:30:06 PDT
